Detection of Binding Site Molecular Interaction Field Similarities.
作者： Matthieu Chartier , Rafael Najmanovich
关键词: Similarity (network science) 、 Receiver operating characteristic 、 Function (mathematics) 、 Data mining 、 Drug toxicity 、 Interaction field 、 Protein family 、 Molecular recognition 、 Biology 、 Computational biology 、 Binding site
摘要: Protein binding-site similarity detection methods can be used to predict protein function and understand molecular recognition, as a tool in drug design for repurposing polypharmacology, the prediction of determinants toxicity. Here, we present IsoMIF, method able identify binding site interaction field similarities across families. IsoMIF utilizes six chemical probes subgraph isomorphisms geometrically chemically equivalent sections cavity pairs. The is validated using distinct data sets, four those previously validation other methods. mean area under receiver operator curve (AUC) obtained sets higher than Furthermore, while obtains consistently high AUC values perform more erratically sets. from structure, detect poten...
acs.org
sci-hub.se 参考文章(67)
Kengo Kinoshita, Haruki Nakamura, Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Science. ,vol. 12, pp. 1589- 1595 ,(2003) , 10.1110/PS.0368703
Howard J Feldman, Paul Labute, Pocket Similarity: Are α Carbons Enough? Journal of Chemical Information and Modeling. ,vol. 50, pp. 1466- 1475 ,(2010) , 10.1021/CI100210C
Abdullah Kahraman, Richard J. Morris, Roman A. Laskowski, Janet M. Thornton, Shape variation in protein binding pockets and their ligands. Journal of Molecular Biology. ,vol. 368, pp. 283- 301 ,(2007) , 10.1016/J.JMB.2007.01.086
Gareth R. Stockwell, Janet M. Thornton, Conformational diversity of ligands bound to proteins. Journal of Molecular Biology. ,vol. 356, pp. 928- 944 ,(2006) , 10.1016/J.JMB.2005.12.012
Stephen M Strittmatter, Overcoming Drug Development Bottlenecks With Repurposing: Old drugs learn new tricks Nature Medicine. ,vol. 20, pp. 590- 591 ,(2014) , 10.1038/NM.3595
Zhu Wang, X Edward Zhou, Daniel L Motola, Xin Gao, Kelly Suino-Powell, Aoife Conneely, Craig Ogata, Kamalesh K Sharma, Richard J Auchus, James B Lok, John M Hawdon, Steven A Kliewer, H Eric Xu, David J Mangelsdorf, Identification of the nuclear receptor DAF-12 as a therapeutic target in parasitic nematodes Proceedings of the National Academy of Sciences of the United States of America. ,vol. 106, pp. 9138- 9143 ,(2009) , 10.1073/PNAS.0904064106
Shelley D. Copley, An evolutionary biochemist's perspective on promiscuity Trends in Biochemical Sciences. ,vol. 40, pp. 72- 78 ,(2015) , 10.1016/J.TIBS.2014.12.004
Valérie Campagna-Slater, Man Wai Mok, Kong T. Nguyen, Miklos Feher, Rafael Najmanovich, Matthieu Schapira, Structural Chemistry of the Histone Methyltransferases Cofactor Binding Site Journal of Chemical Information and Modeling. ,vol. 51, pp. 612- 623 ,(2011) , 10.1021/CI100479Z
Renxiao Wang, Xueliang Fang, Yipin Lu, Chao-Yie Yang, Shaomeng Wang, The PDBbind database: methodologies and updates. Journal of Medicinal Chemistry. ,vol. 48, pp. 4111- 4119 ,(2005) , 10.1021/JM048957Q
Jérémy Desaphy, Karima Azdimousa, Esther Kellenberger, Didier Rognan, Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes Journal of Chemical Information and Modeling. ,vol. 52, pp. 2287- 2299 ,(2012) , 10.1021/CI300184X